BioC 3.4: CHECK report for debrowser on morelia

Package: debrowser

Version: 1.1.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings debrowser_1.1.9.tar.gz

StartedAt: 2016-09-20 05:24:10 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:28:14 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 243.8 seconds

RetCode: 0

Status:  OK

CheckDir: debrowser.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings debrowser_1.1.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/debrowser.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.1.9’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘debrowser’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... NOTE
The following files look like leftovers:
  ‘debrowser/svn-commit.tmp’
Please remove them from your package.
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MAPlot: no visible global function definition for ‘:=’
MAPlot: no visible binding for global variable ‘size’
MAPlot: no visible binding for global variable ‘size.hover’
MAPlot: no visible binding for global variable ‘fillOpacity’
MAPlot: no visible binding for global variable ‘fillOpacity.hover’
MAPlot: no visible binding for global variable ‘fill.brush’
MAPlot: no visible binding for global variable ‘opacity’
MAPlot: no visible binding for global variable ‘key’
MAZoom: no visible global function definition for ‘:=’
MAZoom: no visible binding for global variable ‘size’
MAZoom: no visible binding for global variable ‘size.hover’
MAZoom: no visible binding for global variable ‘key’
getDensityPlot: no visible binding for global variable ‘samples’
getHoverPlots: no visible binding for global variable ‘conds’
getIQRPlot: no visible global function definition for ‘:=’
getIQRPlot: no visible binding for global variable ‘fill’
getSelectedDatasetInput: no visible binding for global variable
  ‘searched’
installpack: no visible global function definition for ‘biocLite’
load_data: no visible binding for global variable ‘demodata’
mainScatter: no visible global function definition for ‘:=’
mainScatter: no visible binding for global variable ‘size’
mainScatter: no visible binding for global variable ‘size.hover’
mainScatter: no visible binding for global variable ‘fillOpacity’
mainScatter: no visible binding for global variable ‘fillOpacity.hover’
mainScatter: no visible binding for global variable ‘fill.brush’
mainScatter: no visible binding for global variable ‘opacity’
mainScatter: no visible binding for global variable ‘key’
plot_pca: no visible global function definition for ‘:=’
runBayseq: no visible binding for global variable ‘fit’
scatterZoom: no visible global function definition for ‘:=’
scatterZoom: no visible binding for global variable ‘size’
scatterZoom: no visible binding for global variable ‘size.hover’
scatterZoom: no visible binding for global variable ‘key’
volcanoPlot: no visible global function definition for ‘:=’
volcanoPlot: no visible binding for global variable ‘size’
volcanoPlot: no visible binding for global variable ‘size.hover’
volcanoPlot: no visible binding for global variable ‘fillOpacity’
volcanoPlot: no visible binding for global variable ‘fillOpacity.hover’
volcanoPlot: no visible binding for global variable ‘fill.brush’
volcanoPlot: no visible binding for global variable ‘opacity’
volcanoPlot: no visible binding for global variable ‘key’
volcanoZoom: no visible global function definition for ‘:=’
volcanoZoom: no visible binding for global variable ‘size’
volcanoZoom: no visible binding for global variable ‘size.hover’
volcanoZoom: no visible binding for global variable ‘key’
Undefined global functions or variables:
  := biocLite conds demodata fill fill.brush fillOpacity
  fillOpacity.hover fit key opacity samples searched size size.hover
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-demo.R’
  Running ‘test-deseq.R’
  Running ‘test-null.R’
  Running ‘test-ui.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/debrowser.Rcheck/00check.log’
for details.

* installing *source* package ‘debrowser’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (debrowser)

name	user	system	elapsed
MAPlot	0.001	0.000	0.000
MAZoom	0.001	0.000	0.000
actionButton	0.003	0.000	0.003
addID	0	0	0
add_title_pos	0.209	0.002	0.233
all2all	0.124	0.002	0.126
applyFilters	0	0	0
applyFiltersToMergedComparison	0	0	0
clusterData	0.000	0.000	0.001
compareClust	0.000	0.000	0.001
deServer	0.009	0.001	0.010
deUI	0.027	0.007	0.222
getAfterLoadMsg	0.001	0.000	0.001
getColors	0.000	0.000	0.001
getCompSelection	0.003	0.001	0.003
getCondMsg	0.000	0.000	0.001
getConditionSelector	0.000	0.000	0.001
getCutOffSelection	0.003	0.000	0.002
getDataForTables	0.000	0.000	0.001
getDataPrepPanel	0	0	0
getDensityPlot	0.000	0.001	0.001
getDomains	0.001	0.000	0.001
getDown	0.001	0.000	0.000
getDownloadSection	0.000	0.000	0.001
getEnrichDO	0	0	0
getEnrichGO	0	0	0
getEnrichKEGG	0.000	0.001	0.001
getGOLeftMenu	0.017	0.002	0.019
getGOPlots	0.000	0.000	0.001
getGeneList	0.857	0.038	0.895
getGeneSetData	0.001	0.000	0.000
getGoPanel	0.001	0.000	0.001
getHelpButton	0.000	0.000	0.001
getHoverPlots	0.001	0.000	0.000
getIQRPlot	0.001	0.000	0.000
getInitialMenu	0.000	0.000	0.001
getIntHeatmap	0.001	0.000	0.000
getIntHeatmapVis	0	0	0
getLeftMenu	0.029	0.004	0.032
getLoadingMsg	0.001	0.000	0.001
getLogo	0.001	0.000	0.001
getMainPanel	0.000	0.000	0.001
getMainPanelPlots	0.000	0.000	0.001
getMean	0	0	0
getMergedComparison	0.001	0.000	0.001
getMethodDetails	0.001	0.000	0.001
getMostVariedList	0.001	0.000	0.000
getNormalizedMatrix	0.019	0.000	0.019
getOrganism	0.001	0.001	0.000
getOrganismBox	0.005	0.000	0.006
getOrganismPathway	0.000	0.000	0.001
getPCAexplained	0.000	0.000	0.001
getPCselection	0.001	0.000	0.001
getProgramTitle	0.001	0.000	0.001
getQCLeftMenu	0.016	0.001	0.017
getQCPanel	0.030	0.002	0.051
getQCPlots	0.000	0.000	0.001
getQCReplot	0.000	0.000	0.001
getSampleNames	0	0	0
getSamples	0.001	0.000	0.001
getSearchData	0.001	0.000	0.000
getSelHeat	0.001	0.000	0.002
getSelectInputBox	0.001	0.000	0.000
getSelectedCols	0.001	0.001	0.001
getSelectedDatasetInput	0	0	0
getStartPlotsMsg	0.003	0.000	0.004
getStartupMsg	0.004	0.000	0.005
getTableStyle	0.000	0.000	0.001
getToolTipPCA	0.000	0.000	0.001
getToolTipText	0.001	0.000	0.000
getUp	0.001	0.000	0.000
getUpDown	0.001	0.000	0.001
hideObj	0.001	0.000	0.001
installpack	0.001	0.000	0.001
link_brush	0.004	0.000	0.005
load_data	0.000	0.001	0.001
logSliderJScode	0.000	0.000	0.001
mainScatter	0.001	0.000	0.000
panel.cor	0.002	0.000	0.001
panel.hist	0.001	0.000	0.002
plot_pca	1.508	0.027	1.536
prepAddQCPlots	0.001	0.000	0.001
prepDEOutput	0	0	0
prepDataContainer	0.000	0.000	0.001
prepDataForQC	0	0	0
push	0.001	0.000	0.000
removeCols	0.001	0.000	0.001
round_vals	0	0	0
runBayseq	0.000	0.000	0.001
runDE	0.000	0.000	0.001
runDESeq	0.001	0.000	0.000
runDESeq2	0.001	0.000	0.001
runEdgeR	0.000	0.000	0.001
runHeatmap	0.116	0.005	0.121
runLimma	0.001	0.000	0.001
run_pca	0.820	0.034	0.854
saveQCPlot	0.000	0.000	0.001
scatterZoom	0.000	0.000	0.001
selectConditions	0.000	0.001	0.000
selectedInput	0	0	0
setFilterParams	0.000	0.000	0.001
showObj	0.001	0.000	0.001
startDEBrowser	0.001	0.000	0.000
textareaInput	0.001	0.000	0.000
togglePanels	0.000	0.000	0.001
volcanoPlot	0.001	0.000	0.000
volcanoZoom	0.000	0.000	0.001